In this paper, we examine the effect of the nanostructures on the parallel-plate microchannel flow experimentally as well as the nanochannel flow based on molecular dynamic studies. In the experiments, the microchannel surface is coated with nanostructures using plating and etching, and the sizes of nanostructures are rather different from the conventional surface roughness. The spacing of the parallel-plate microchannel is 300 μm, which is much smaller than its width and length, in order to reduce the effects of sidewalls as a well-studied geometry. It is found that the friction constant for the nanostructured surfaces of large contact angle (hydrophobility) is low compared with the surfaces of small contact angle (hydrophility). Also, the higher heat transfer coefficients have been obtained at the hydrophilic nanostructured surface with characteristic size of nanostructure of 200–700nm. In the molecular dynamics simulations of nanochannel flow, it is found that both the boundary condition at the solid-liquid interface depend on the surface wettability. The interface thermal resistance decreases at the nanostructured surface and significant heat transfer enhancement has been achieved at the nanostructured surfaces of hydrophility. Although the surface with nanostructures has larger surface area than the flat surface, the rate of heat flux increase caused by the nanostructures is still remarkable; however, it is unclear if the effect of the nanostructures could be detected in the microchannel experiments. [ABSTRACT FROM AUTHOR]